[gmx-users] Fatal error: Number of atoms in Topology is not the same as in Trajectory

[Shima Arasteh]

Dear all,

I have a system of POPC/Protein/water/ions to simulate. I am trying to simulate this system by getting ideas from Justin's tutorial of kalp15-dppc.
I've passed all steps of EM, NVT, and NPT as I expected. But when I want to run mdrun, I get some errors about waters can not be settle. So, I tried to remove them from npt.gro, update the number of atoms in .gro file, and then update number of SOL molecules in top file.Finally I made a new index file to go on.

Next, to start mdrun, I run this command: 

grompp -f md.mdp -c npt.gro -t npt.cpt -p topol.top -n index-new.ndx -o md_0_1.tpr
and get this fatal error:
Number of atoms in Topology is not the same as in Trajectory.

In fact, I thought of updating npt.cpt file, but it's a binary file and I guess it's impossible. Does anybody knows what should I do?  Would you please give me advice?

Thanks in advance.

 
Sincerely,
Shima